LOCUS       NZ_CP033211             4453 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Enterococcus faecium strain RBWH1 plasmid pRBWH1.5, complete
            sequence.
ACCESSION   NZ_CP033211
VERSION     NZ_CP033211.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10273305
            Assembly: GCF_003957785.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4453)
  AUTHORS   Bohlmann,L., De Oliveira,D.M.P., El-Deeb,I.M., Brazel,E.B.,
            Harbison-Price,N., Ong,C.Y., Rivera-Hernandez,T., Ferguson,S.A.,
            Cork,A.J., Phan,M.D., Soderholm,A.T., Davies,M.R., Nimmo,G.R.,
            Dougan,G., Schembri,M.A., Cook,G.M., McEwan,A.G., von Itzstein,M.,
            McDevitt,C.A. and Walker,M.J.
  TITLE     Chemical Synergy between Ionophore PBT2 and Zinc Reverses Antibiotic
            Resistance
  JOURNAL   mBio 9 (6), e02391-18 (2018)
   PUBMED   30538186
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4453)
  AUTHORS   Bohlmann,L., De Oliviera,D., El-Deeb,I., Brazel,E.,
            Harbison-Price,N., Ong,C.-L., River-Hernandez,T., Ferguson,S.,
            Cork,A., Phan,M.-D., Davies,M., Nimmo,G., Dougan,G., Schembri,M.,
            Cook,G., McEwan,A., von Itzstein,M., McDevitt,C. and Walker,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2018) Department of Microbiology and Immunology,
            University of Melbourne, The Doherty Institute of Infection and
            Immunology, Melbourne, Victoria 3000, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: PacBio SMRT Pipe v. 2.3.0
            Assembly Name                     :: RBWH1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/17/2023 02:36:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,093
            CDSs (total)                      :: 3,001
            Genes (coding)                    :: 2,878
            CDSs (with protein)               :: 2,878
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 44 of 123
            Pseudo Genes (incomplete)         :: 77 of 123
            Pseudo Genes (internal stop)      :: 24 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033211.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4453
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="RBWH1"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pRBWH1.5"
                     /geo_loc_name="Australia: Brisbane"
                     /collection_date="2016"
                     /collected_by="Royal Brisbane Women's Hospital"
     gene            1..738
                     /gene="erm(B)"
                     /locus_tag="EBB55_RS16170"
                     /old_locus_tag="EBB55_16170"
     ARG             2..735
                     /name="erm(B)"
                     /gene="erm(B)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(B)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="99.59"
                     /coverage="100.0"
     gene            complement(1001..1864)
                     /locus_tag="EBB55_RS16175"
                     /old_locus_tag="EBB55_16175"
     CDS             complement(1001..1864)
                     /locus_tag="EBB55_RS16175"
                     /old_locus_tag="EBB55_16175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010782381.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016301 - kinase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="zeta toxin family protein"
                     /protein_id="WP_001284311.1"
                     /translation="MANIVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSG
                     KTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIIS
                     RLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMY
                     ADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISP
                     KETLEKELNRKVSGKEIQPTLERIEQKMVLNKHQETPEFKAIQQKLESLQPPTPPIPKT
                     PKLPGI"
                     /name="zeta toxin family protein"
     gene            complement(1866..2138)
                     /locus_tag="EBB55_RS16180"
                     /old_locus_tag="EBB55_16180"
     CDS             complement(1866..2138)
                     /locus_tag="EBB55_RS16180"
                     /old_locus_tag="EBB55_16180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002333002.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin"
                     /protein_id="WP_000301765.1"
                     /translation="MAVTYEKTFEIEIINELSASVYNRVLNYVLNHELNKNDSQLLEVN
                     LLNQLKLAKRVNLFDYSLEELQAVHEYWRSMNRYSKQVLNKEKVA"
                     /name="antitoxin"
     gene            complement(2155..2370)
                     /locus_tag="EBB55_RS16185"
                     /old_locus_tag="EBB55_16185"
     CDS             complement(2155..2370)
                     /locus_tag="EBB55_RS16185"
                     /old_locus_tag="EBB55_16185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002401482.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="peptide-binding protein"
                     /protein_id="WP_001835296.1"
                     /translation="MIVGNLGAQKAKRNDTPISAKKDIMGDKTVRVRADLHHIIKIETA
                     KNGGNVKEVMDQALEEYIRKYLPDKL"
                     /name="peptide-binding protein"
     gene            <2566..2817
                     /locus_tag="EBB55_RS16190"
                     /old_locus_tag="EBB55_16190"
                     /pseudo=""
     CDS             <2566..2817
                     /locus_tag="EBB55_RS16190"
                     /old_locus_tag="EBB55_16190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000627290.1"
                     /GO_function="GO:0008080 - N-acetyltransferase activity
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="GNAT family N-acetyltransferase"
                     /name="GNAT family N-acetyltransferase"
     gene            2910..3704
                     /gene="aph(3')-IIIa"
                     /locus_tag="EBB55_RS16195"
                     /old_locus_tag="EBB55_16195"
     ARG             2911..3701
                     /name="aph(3')-IIIa"
                     /gene="aph(3')-IIIa"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3')-IIIa"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            <4114..4197
                     /locus_tag="EBB55_RS16775"
                     /old_locus_tag="EBB55_16200"
                     /pseudo=""
     CDS             <4114..4197
                     /locus_tag="EBB55_RS16775"
                     /old_locus_tag="EBB55_16200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000502600.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MLS leader peptide"
                     /name="MLS leader peptide"
     gene            4246..4329
                     /locus_tag="EBB55_RS16205"
                     /old_locus_tag="EBB55_16205"
     CDS             4246..4329
                     /locus_tag="EBB55_RS16205"
                     /old_locus_tag="EBB55_16205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001814874.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S rRNA methyltransferase attenuator leader
                     peptide ErmL"
                     /protein_id="WP_031929417.1"
                     /translation="MLVFQMRYVDKTSTVLKQTKNSDYADK"
                     /name="23S rRNA methyltransferase attenuator leader peptide
                     ErmL"
     ARG             2..738
                     /name="ErmB"
                     /gene="ErmB"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="98.78"
                     /coverage="98.79"
ORIGIN
        1 atgaacaaaa atataaaata ttctcaaaac tttttaacga gtgaaaaagt actcaaccaa
       61 ataataaaac aattgaattt aaaagaaacc gataccgttt acgaaattgg aacaggtaaa
      121 gggcatttaa cgacgaaact ggctaaaata agtaaacagg taacgtctat tgaattagac
      181 agtcatctat tcaacttatc gtcagaaaaa ttaaaactga atactcgtgt cactttaatt
      241 caccaagata ttctacagtt tcaattccct aacaaacaga ggtataaaat tgttgggaat
      301 attccttacc atttaagcac acaaattatt aaaaaagtgg tttttgaaag ccgtgcgtct
      361 gacatctatc tgattgttga agaaggattc tacaagcgta ccttggatat tcaccgaaca
      421 ctagggttgc tcttgcacac tcaagtctcg attcagcaat tgcttaagct gccagcggaa
      481 tgctttcatc ctaaaccaaa agtaaacagt gtcttaataa aacttacccg ccataccaca
      541 gatgttccag ataaatattg gaagctatat acgtactttg tttcaaaatg ggtcaatcga
      601 gaatatcgtc aactgtttac taaaaatcag tttcatcaag caatgaaaca cgccaaagta
      661 aacaatttaa gtaccgttac ttatgagcaa gtattgtcta tttttaatag ttatctatta
      721 tttaacggga ggaaataatt ctatgagtcg cttttgtaaa tttggaaagt tacacgttac
      781 taaagggaat gtagataaat tattaggtat agggcacctc taataactac caattaattc
      841 acctcaaaat gaaattagaa aaaaacagcg aaatttttaa atctatttct tatcgataca
      901 aattcctcgt aggcgctcgg gaccccaaca tgaggaaatg tttttataaa aaaagagtag
      961 ttaccgtttt ttggtaacta ctcttttcct tttttaaggt ttaaatacct ggaagtttag
     1021 gtgttttggg tattggtggt gtaggtggct gcaagctttc caatttttgt tgaattgctt
     1081 taaattcagg tgtctcttgg tgtttattta gaaccatttt ttgctctatt cgttctaaag
     1141 tcggttgaat ttctttccct gatactttac gattcaattc tttttctaag gtttcttttg
     1201 gactaataga aggtgtttcc aaacttgaat agagttttac tccttctctg ttatatagcc
     1261 ttatatcgct aaataagccc gttttatgaa gggtttctaa attggtcggt aagtttttga
     1321 caacaatatc atgcgcttgt tttggtgttg ccctggctgt cattggatca tctgcataca
     1381 tggtttcata tcgttcaatt gttcctaaat atgagttgat tttaggtact gccatgacat
     1441 acatttttgt ttcataacct ttggcttgaa gcattgttgc ggtttgaata ggaacgtctg
     1501 ttgttcgtcc tgtaccttcg atcaccaaat tatacccttg atcgctcaaa cggcttatga
     1561 tcgcttctgt catgcgatta gaataagggg taacgtgttt tactacgtct ttttcataaa
     1621 gtttcactag ttcatcaaaa ttagggtgct gttgtttaaa ggtatcatta tcaatgacaa
     1681 taacattccc ttgtgtttct tcaaaaattg ctgatcgcaa actggttttc cctgaccctg
     1741 gttgcccacc aagtaaaaaa gcggttggcg attcaaccgc tttttttcct tgaatcaatt
     1801 cttctaaatt atcatttaag cgattctcaa attgtttgtc agtaaaattg actatatttg
     1861 ccatattaag ccactttctc tttattcaaa acttgttttg agtaacgatt cattgaccgc
     1921 caatactcat gaacggcttg taattcttct aaagaataat caaaaagatt tacacgtttt
     1981 gcaagcttta attggtttaa taaattgact tccaataatt gagagtcatt tttatttaat
     2041 tcatggttca aaacatagtt taatactcga ttataaacgc ttgccgataa ttcgttaatg
     2101 atctctattt caaatgtttt ttcatacgta actgccattt cattttcact ccttttaaag
     2161 tttgtcaggt aaatatttcc gtatatattc ttctaaggct tgatccataa cttcttttac
     2221 gtttccgcca ttctttgctg tttcgatttt tatgatatgg tgcaagtcag cacgaacacg
     2281 aaccgtctta tctcccatta tatctttttt tgcactgatt ggtgtatcat ttcgttttgc
     2341 tttttgtgcg cctaaatttc ccacaatcac tcacttcttt ctatttcttc ttactcttat
     2401 tttatcatca acaatcacaa atcacaagtg atttgtgatt aatcacttgt gatttgtgat
     2461 tctattcttt ttcgggttct gttgcaaagt tttaaataaa gaataaaatc atactagaga
     2521 ggctccgttc tcgtgtgatc gtagatttgt ataagataca tcttttatat agaagatatc
     2581 gccgtatgta aggatttcag ggggcaaggc ataggcagcg cgcttatcaa tatatctata
     2641 gaatgggcaa agcataaaaa cttgcatgga ctaatgcttg aaacccagga caataacctt
     2701 atagcttgta aattctatca taattgtggt ttcaaaatcg gctccgtcga tactatgtta
     2761 tacgccaact ttgaaaacaa ctttgaaaaa gctgttttct ggtatttaag gttttagaat
     2821 gcaaggaaca gtgaattgga gttcgtcttg ttataattag cttcttgggg tatctttaaa
     2881 tactgtagaa aagaggaagg aaataataaa tggctaaaat gagaatatca ccggaattga
     2941 aaaaactgat cgaaaaatac cgctgcgtaa aagatacgga aggaatgtct cctgctaagg
     3001 tatataagct ggtgggagaa aatgaaaacc tatatttaaa aatgacggac agccggtata
     3061 aagggaccac ctatgatgtg gaacgggaaa aggacatgat gctatggctg gaaggaaagc
     3121 tgcctgttcc aaaggtcctg cactttgaac ggcatgatgg ctggagcaat ctgctcatga
     3181 gtgaggccga tggcgtcctt tgctcggaag agtatgaaga tgaacaaagc cctgaaaaga
     3241 ttatcgagct gtatgcggag tgcatcaggc tctttcactc catcgacata tcggattgtc
     3301 cctatacgaa tagcttagac agccgcttag ccgaattgga ttacttactg aataacgatc
     3361 tggccgatgt ggattgcgaa aactgggaag aagacactcc atttaaagat ccgcgcgagc
     3421 tgtatgattt tttaaagacg gaaaagcccg aagaggaact tgtcttttcc cacggcgacc
     3481 tgggagacag caacatcttt gtgaaagatg gcaaagtaag tggctttatt gatcttggga
     3541 gaagcggcag ggcggacaag tggtatgaca ttgccttctg cgtccggtcg atcagggagg
     3601 atatcgggga agaacagtat gtcgagctat tttttgactt actggggatc aagcctgatt
     3661 gggagaaaat aaaatattat attttactgg atgaattgtt ttagtaccta gatttagatg
     3721 tctaaaaagc tttaactaca agctttttag acatctaatc ttttctgaag tacatccgca
     3781 actgtccata ctctgatgtt ttatatcttt tctaaaagtt cgctagatag gggtcccgag
     3841 cgcctacgag gaatttgtat cgataagaaa tagatttaaa aatttcgctg ttattttgta
     3901 catttaactt gacggtgaca tctctctatt gtgagttatt agtggtacag ttttcaaccg
     3961 ttttaattat aaaaaagtgg tgcattttta aattggcaca aacaggtaac ggttattgca
     4021 ggtgtatttc ttatctatgg gtttaacatg gattttatca ttaaaatcat gagtattgtc
     4081 cgagagtgat tggtcttgcg tatggttaac cctaaagtta tggaaataag acttagaagc
     4141 aaacttaaga gtgtgttgat agtgcattat cttaaaattt tgtataatag gaattgaagt
     4201 taaattagat gctaaaaatt tgtaattaag aaggagggat tcgtcatgtt ggtattccaa
     4261 atgcgttatg tagataaaac atctactgtt ttgaaacaga ctaaaaacag tgattacgca
     4321 gataaataaa tacgttagat taattcctac cagtgactaa tcttatgact ttttaaacag
     4381 ataactaaaa ttacaaacaa atcgtttaac ttctgtattt gtttatagat gtaatcactt
     4441 caggagtgat aac
//
